Crate wdl_lint 

Lint rules for Workflow Description Language (WDL) documents.

Rules

This table documents all sprocket lint rules implemented on the main branch of the stjude-rust-labs/sprocket repository. Note that the information may be out of sync with released packages.

Lint Rules

Name	Tags	Description	Config
CallInputSpacing	Spacing, Style	Ensures that call inputs are spaced appropriately.
CallInputKeyword	Deprecated, Style	Ensures that the input: keyword is not used in call statements when WDL version is 1.2 or later.
CommandSectionIndentation	Spacing, Clarity, Correctness	Ensures consistent indentation (no mixed spaces/tabs) within command sections.
CommentWhitespace	Spacing, Style	Ensures that WDL comments have the proper spacing.
ConciseInput	Style	Ensures concise input assignments are used (implicit binding when available).
ConsistentNewlines	Spacing, Clarity, Portability	Ensures that newline usage is consistent.
ContainerUri	Clarity, Portability	Ensures that values for the container key within runtime/requirements sections are well-formed.
DeclarationName	Naming, Style, Clarity	Ensures declaration names do not redundantly include their type name.
DeprecatedObject	Deprecated	Ensures that the deprecated Object types are not used.
DeprecatedPlaceholder	Deprecated	Ensures that deprecated expression placeholder options are not used.
DescriptionLength	SprocketCompatibility	Ensures that description meta entries are not too long for display in Sprocket documentation
DocMetaStrings	SprocketCompatibility	Ensures that reserved meta keys have string values for wdl-doc compatibility
DoubleQuotes	Style, Clarity	Ensures that strings are defined using double quotes.
ElementSpacing	Spacing, Style	Ensures that WDL elements are spaced appropriately.
EndingNewline	Spacing, Portability	Ensures that documents end with a single newline character.
ExpectedRuntimeKeys	Completeness, Deprecated	Ensures that runtime sections have the appropriate keys.	* allowed_runtime_keys - A list of keys to ignore.
ExpressionSpacing	Spacing, Style	Ensures that WDL expressions are properly spaced.
HereDocCommands	Clarity, Correctness	Ensures that tasks use heredoc syntax in command sections.
ImportPlacement	Clarity	Ensures that imports are placed between the version statement and any document items.
ImportSorted	Sorting	Ensures that imports are sorted lexicographically.
ImportWhitespace	Spacing, Style	Ensures that there is no extraneous whitespace between or within imports.
InputName	Naming, Style	Ensures input names are meaningful (e.g. not generic like ‘input’, ‘in’, or too short).
InputSorted	Sorting	Ensures that input declarations are sorted
KnownRules	Clarity, Correctness, SprocketCompatibility	Ensures only known rules are used in lint directives.
LineWidth	Spacing, Style	Ensures that lines do not exceed a certain width.
LintDirectiveFormatted	Clarity, Correctness, SprocketCompatibility	Ensures lint directives are correctly formatted.
LintDirectiveValid	Clarity, Correctness, SprocketCompatibility	Ensures lint directives are placed correctly to have the intended effect.
MatchingOutputMeta	Completeness, Documentation, SprocketCompatibility	Ensures that each output field is documented in the meta section under meta.outputs.
MetaDescription	Completeness, Documentation, SprocketCompatibility	Ensures the meta section contains a description key
MetaKeyValueFormatting	Spacing, Style	Ensures that arrays and objects in meta and parameter_meta sections have one element per line and are indented correctly.
MetaSections	Completeness, Clarity, Documentation	Ensures that tasks and workflows have the required meta and parameter_meta sections.
OutputName	Naming, Style	Ensures output names are meaningful (e.g. not generic like ‘output’, ‘out’, or too short).
ParameterMetaMatched	Completeness, Sorting, Documentation, SprocketCompatibility	Ensures that inputs have a matching entry in a parameter_meta section.
PascalCase	Naming, Style, Clarity	Ensures that structs are defined with PascalCase names.
PreambleCommentPlacement	Style, Clarity, SprocketCompatibility	Ensures that preamble comments are inside the preamble.
PreambleFormatted	Spacing, Style, SprocketCompatibility	Ensures that documents have correct formatting in the preamble.
RedundantNone	Style	Flags redundant assignment of None to optional inputs.
RequirementsSection	Completeness, Portability, Deprecated	Ensures that tasks have a requirements section (for WDL v1.2 and beyond).
RuntimeSection	Completeness, Portability	Ensures that tasks have a runtime section (for WDL v1.1 and prior).
SectionOrdering	Style, Sorting	Ensures that all sections are in the correct order.
ShellCheck	Correctness	Ensures that command blocks are free of ShellCheck violations.
SnakeCase	Naming, Style, Clarity	Ensures that tasks, workflows, and variables are defined with snake_case names.
TodoComment	Style	Flags TODO statements in comments to ensure they are not forgotten.
TrailingComma	Style	Ensures that lists and objects have a trailing comma and that there’s not extraneous whitespace and/or comments before the trailing comma.
VersionStatementFormatted	Spacing, Style	Ensures the version statement is correctly formatted.
Whitespace	Spacing, Style	Ensures that a document does not contain undesired whitespace.

Definitions

Definitions

WDL Document Structure

Preamble

The document preamble is defined as anything before the version declaration statement and the version declaration statement itself. Only comments and whitespace are permitted before the version declaration.

Comment Types

Lint Directives

Lint directives are special comments that begin with #@ except: followed by a comma-delimited list of rule IDs. These comments are used to disable specific lint rules for a section of the document. When a lint directive is encountered in the preamble, it will disable the specified rules for the entire document.

For example:

#@ except: LineWidth, CommentWhitespace

Preamble Comments

Preamble comments are special comments at the start of a WDL file that begin with double pound signs (##). These comments are used for documentation that doesn’t fit within any of the WDL-defined documentation elements (i.e., meta and parameter_meta sections). They may provide context for a collection of tasks or structs, or they may provide a high-level overview of a workflow. Preamble comments can be formatted as Markdown text.

For example:

## # FlagFilter
##
## A struct to represent the filtering flags used in various `samtools` commands.

Examples

An example of parsing a WDL document and linting it:

use wdl_lint::Linter;
use wdl_lint::analysis::Validator;
use wdl_lint::analysis::document::Document;

let mut validator = Validator::default();
validator.add_visitor(Linter::default());

Re-exports

pub use wdl_analysis as analysis;

pub use wdl_ast as ast;

Modules

rules

Module for the lint rules.

Structs

Config

The configuration for lint rules.

Linter

A visitor that runs linting rules.

TagSet

A set of lint tags.

UnknownTagError

An error for when an unknown tag is encountered.

Enums

Tag

A lint rule tag.

Constants

DEFINITIONS_TEXT

The definitions of WDL concepts and terminology used in the linting rules.

Statics

ALL_RULE_IDS

All rule IDs sorted alphabetically.

ALL_TAG_NAMES

All tag names sorted alphabetically.

Traits

Rule

A trait implemented by lint rules.

Functions

find_nearest_rule

Finds the nearest rule ID to the given unknown rule ID, or None if no rule ID is close enough.

rules

Gets all of the lint rules.